biochemical-networks

There are 0 repository under biochemical-networks topic.

biosimulations
biosimulations / biosimulations
A platform for sharing and reusing biomodeling studies including models, simulations, and visualizations of their results
biology modeling simulation standards sbml sed-ml vega reproducibility biochemical-networks biosimulations biological-simulations biosimulation
Language:TypeScript 36
biomass
biomass-dev / biomass
A Python Framework for Modeling and Analysis of Signaling Systems
python systems-biology computational-biology simulation kinetic-modeling parameter-estimation ode biochemical-networks dynamical-systems ordinary-differential-equations systems-biology-simulation modeling optimization network-analysis
Language:Python 24
pasmopy
pasmopy / pasmopy
Patient-Specific Modeling in Python
systems-biology cancer personalized-medicine kinetic-modeling patient-specific-modeling python computational-biology systems-biology-simulation precision-medicine precision-oncology in-silico-clinical-trial biochemical-networks digital-twin
Language:Python 16
BhallaLab / FindSim
FindSim - A Framework for Integrating Neuronal Data and Signaling Models
biochemical-networks moose model-estimation signalling
Language:GAP 7
Biosimulators_test_suite
biosimulators / Biosimulators_test_suite
Tool for validating that biosimulation software tools implement the BioSimulators standards for simulators
systems-biology mathematical-modelling computational-biology sbml cellml sed-ml docker biosimulators combine-archive omex-metadata simulation biochemical-networks simulator research
Language:Python 7
MetEvolSim
charlesrocabert / MetEvolSim
MetEvolSim (Metabolome Evolution Simulator). A Python package to simulate the long-term evolution of metabolic levels.
biochemical-networks copasi evolution metabolic-abundances metabolic-network metabolome sbml simulation systems-biology
Language:Python 5
draeger-lab / SBMLsqueezer
Context-sensitive creation of kinetic equations in biochemical networks
biological-networks information-extraction mathematical-modelling metabolic-engineering regulatory-network computational-biology systems-biology andreas-zell biochemical-networks andreas-dr-ger kinetic-equations sbo bmc-systems-biology plug equation reactions celldesigner reaction sbml
Language:HTML 4
Biosimulators_COBRApy
biosimulators / Biosimulators_COBRApy
COBRApy biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
cobrapy sbml sed-ml combine-archive flux-balance-analysis fba systems-biology computational-biology constraint-based-modeling biochemical-networks simulation omex-metadata docker biosimulators python
Language:Python 2
Biosimulators_COPASI
biosimulators / Biosimulators_COPASI
COPASI biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
copasi dynamical-modeling sed-ml combine-archive omex-metadata sbml biochemical-networks systems-biology computational-biology simulation docker biosimulators python
Language:Python 2
Biosimulators_BioNetGen
biosimulators / Biosimulators_BioNetGen
BioNetGen biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
systems-biology rule-based-modeling network-free-simulation simulation bionetgen sed-ml combine-archive omex-metadata stochastic-simulation-algorithm biochemical-networks dynamical-modeling docker biosimulators
Language:Python 1
Biosimulators_GillesPy2
biosimulators / Biosimulators_GillesPy2
GillesPy2 biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
systems-biology computational-biology biochemical-networks stochastic-simulation-algorithm sbml sed-ml combine-archive gillespy2 stochss stochkit simulation omex-metadata dynamical-modeling docker biosimulators python
Language:Python 1
Biosimulators_tellurium
biosimulators / Biosimulators_tellurium
tellurium biochemical network simulation program via BioSimulators-compliant command-line interface and Docker container
biochemical-networks biosimulators combine-archive computational-biology docker dynamical-modeling libroadrunner omex-metadata python sbml sed-ml simulation systems-biology tellurium
Language:Python 1
bradduthie / RandomMatrixStability
R package associated with paper "Component response rate variation underlies the stability of highly complex finite systems" (Duthie, AB. 2020. Sci. Rep. 10:8296, https://www.nature.com/articles/s41598-020-64401-w). This repository contains all manuscript text and supplemental information, and all code for recreating analyses.
network-theory random-matrix-theory ecological-network biological-networks stability biochemical-networks complex-networks complex-systems interaction-dynamics
Language:HTML 1
AGCT-DSL / AGCT
Another Genetic Circuit Transcriber
biochemistry biochemical biochemical-reactions biochemical-networks genetic-circuits genetics dsl domain-specific-language genetic-regulatory-network genetic kotlin-dsl kotlin
Language:Kotlin 0
biomass-dev / BioMASS.jl
Julia interface to BioMASS
julia systems-biology modeling parameter-estimation differential-equations bifurcation dynamical-systems simulation kinetic-modeling computational-biology biochemical-networks systems-biology-simulation bifurcation-diagram continuation
Language:Julia 0
JRC-COMBINE / TROSS
Tropical Sensitivity Scores
tropical-geometry numerical-methods biochemical-networks biochemical-reactions perturbations
Language:R 0
manvelgasparyan / settling_time
This repository is used to determine the settling time of a given biochemical reaction network using the approach described in the manuscript "An Automated Model Reduction Method for Biochemical Reaction Networks" published in "Symmetry".
chemical-reactions biochemical-networks biochemical-reactions systems-biology mathematical-modelling steady-state
Language:MATLAB 0